Project description:A targeted RNA-based method for typing of 12 classical HLA genes using Oxford Nanopore sequencing. In the method, were enriched HLA genes from cDNA of 50 individuals using gene-specific reverse primers. The library molecules were then barcoded, pooled into 2 separate gene pools, and sequenced on MinION R9.4 SpotON flow cells.
Project description:Genomic DNA contains next to the four canonical nucleosides dA, dC, dG and T the additional base 5-methyldeoxycytidine (mdC). The presence of this methylated cytidine nucleoside in promoter regions or gene bodies has an instrumental effect on the transcriptional activity of the corresponding gene. The methylation patterns of genes are therefore responsible for either silencing or activation of genes. Sequencing of mdC positions in the genome is consequently of paramount importance for early cancer diagnostics in order to determine incorrect expression of genes. Today, the bisulfite method is the gold standard for mdC-sequencing, which has however the caveat that the majority of the input DNA is degraded during the bisulfite treatment. In addition, bisulfite sequencing is rather error prone. Here we report a benign, bisulfite free mdC sequencing method based on 3rd generation single molecule SMRT sequencing. The fundament of the technology is a new Tet3 enzyme that oxidizes mdCs with high efficiency to 5-carboxycytidine (cadC). caC in turn provides and excellent read out by SMRT sequencing using specially trained AI-based algorithms.
Project description:HLA typing of a family (patient and his mother) for donor selection to haploidential transplantation of hematopoetic stem cells(HSC) 1140-1, 1140-2
Project description:HLA typing of a family (patient and his father) for donor selection to haploidential transplantation of hematopoetic stem cells(HSC) 1434-1, 1434-3
Project description:HLA typing of a family (patient and his mother) for donor selection to haploidential transplantation of hematopoetic stem cells(HSC) 1432-1, 1432-3
